Now the question is, if half of the new drug approvals came from only one trial, while at the same time the FDA states that one trial approvals should be a rare exception, what explains this conflict?

Maybe there are just more applications for diseases with no current standard of care? Or maybe the FDA just has a funny definition of rare. They also stated this in their report - 73% of applications were given priority review. 73% sounds more like standard review than priority to me.